brain_extraction {rpyANTs} | R Documentation |
Extract brain and strip skull
Description
Function brain_mask
and brain_extraction
use the ants
base package.
Function antspynet_brain_extraction
uses antspynet
to extract
the brain using deep neural network. This requires additional configuration.
Print antspynet$brain_extraction
to see the original documentation.
Usage
antspynet_brain_extraction(
x,
modality = c("t1", "t1nobrainer", "t1combined", "flair", "t2", "t2star", "bold", "fa",
"t1t2infant", "t1infant", "t2infant"),
verbose = FALSE
)
brain_mask(
x,
work_path = tempfile(pattern = "rpyant_brain_extraction_"),
verbose = TRUE,
auto_clean = TRUE
)
brain_extraction(
x,
skull_alpha = 0,
threshold_quantile = 0.85,
...,
verbose = TRUE
)
Arguments
x |
input image or image path |
modality |
modality type, used by |
verbose |
whether to print out process to the screen |
work_path |
working directory; default is temporary path |
auto_clean |
whether to automatically clean the working path if the path is temporary; default is true |
skull_alpha |
used by |
threshold_quantile |
used only when |
... |
see |
Value
brain_mask
Brain mask image
brain_extraction
extracted brain
antspynet_brain_extraction
Brain mask image